2024-10-30 REL PDBj PDBj PDBj 2022-06-21 2023-08-02 2023-08-02 2024-10-30 National Research Foundation (NRF, Singapore) NRF2016NRF-NSFC002-013 Singapore Other government STPRG-FY19-001 Singapore Other government COVID19RF-003 Singapore Other government COVID19RF-060 Singapore Other government MOH-000535/MOH-OFYIRG19nov-0002 Singapore Other government OFLCG19May-0034 Singapore National Health and Medical Research Council (NHMRC, Australia) GNT 2008092 Australia Damon Runyon Cancer Research Foundation United States SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 (focused refinement on Fab-RBD interface) Chia WN Tan CW Tan AWK Young B Starr TN Lopez E Fibriansah G Barr J Cheng S Yeoh AYY Yap WC Lim BL Ng TS Sia WR Zhu F Chen S Zhang J Greaney AJ Chen M Au GG Paradkar P Peiris M Chung AW Bloom JD Lye D Lok SM Wang LF VIRAL PROTEIN Chia WN Tan CW Tan AWK Young B Starr TN Lopez E Fibriansah G Barr J Cheng S Yeoh AY Yap WC Lim BL Ng TS Sia WR Zhu F Chen S Zhang J Kwek MSS Greaney AJ Chen M Au GG Paradkar PN Peiris M Chung AW Bloom JD Lye D Lok S Wang LF Potent pan huACE2-dependent sarbecovirus neutralizing monoclonal antibodies isolated from a BNT162b2-vaccinated SARS survivor. Sci Adv US 9 eade3470 eade3470 2023 37494438 doi:10.1126/sciadv.ade3470 2375-2548 7y72 FULLOVERLAP SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 0 1 2 3 Homo sapiens Spike glycoprotein Homo sapiens 0.13286015599999998 2 Homo sapiens LEVO VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFAST EKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS SGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNL CPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQT GKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSY GFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEH VNNSYECDIPIGAGICASYQTQTNSPRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTS VDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKR SPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQ IPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNFGAISS VLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQS APHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNN TVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP P0DTC2 Fab E7 light chain Homo sapiens 0.023920668 1 Homo sapiens LEVO DIVMTQSPLSLPVTPGEPASISCRSSQSLLQNNGYNYLAWYLQKPGQSPQLLIYLSSTRASGVPDRFSGSGSGTDFTLKI SRVEAEDVGVYYCMQSLQIPGTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQ SGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC Fab E7 heavy chain Homo sapiens 0.023339155999999996 1 Homo sapiens LEVO QVQLQESGPGLVKPSETLSLTCTVSGGFIGPHYWSWVRQPPGKGLEWIGYIYISGSTNYNPSLKSRLTISVDMSKSQFSL TLSSATAADTAVYYCARGGGYLETGPFEYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK singleParticle particle 7.4 50.0 NH2C(CH2OH)3 Tris buffer 300.0 NaCl Sodium chloride UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE ETHANE 100 277.15 FEI VITROBOT MARK IV
SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.4 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 1 4.76 31.6
Images were collected in counting mode at 25 frames per movie with an exposure time of 4.76 s per movie.
 1 402809 Ab initio model
cryoSPARC was used to generate an ab initio model.
 C1 4.03 FSC 0.143 CUT-OFF cryoSPARC 3.3.1+220215
Local refinement in cryoSPARC
198525 MAXIMUM LIKELIHOOD RELION 4.0-beta-2-commit-543db0
Heterogeneous refinement in cryoSPARC
 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1+220215
Non-uniform refinement followed by local refinement in cryoSPARC
 emd_33651.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 397.80002 397.80002 397.80002 90.0 90.0 90.0 X Y Z -58.422398000000001 124.104680000000002 0.00000000041966 1.0 1.105 1.105 1.105 7.55 AUTHOR Focused refinement of SARS-CoV-2 spike (S) protein receptor binding domains (RBDs) in complex with anti-RBD Fab E7 6XKL PDB experimental model 6N16 A 114-213 PDB experimental model 6N16 B 108-212 PDB experimental model REAL emd_33651_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 397.80002 397.80002 397.80002 90.0 90.0 90.0 X Y Z -0.7389175 2.0438066 0.0009008481 0.045724142 1.105 1.105 1.105 AUTHOR emd_33651_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 397.80002 397.80002 397.80002 90.0 90.0 90.0 X Y Z -0.7218133 1.5360484 0.00090277015 0.044790898 1.105 1.105 1.105 AUTHOR